Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: Extractor
https://packages.ecosyste.ms/registries/pypi.org/packages/Extractor
bindings for GNU libextractor, the metadata extractor
1 version
Latest release: over 18 years ago
250 downloads last month
Papers Mentioning Extractor 49
10.1186/s13072-016-0064-6
Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencingCited by: 59
Author(s): Andrew Keniry, Linden J. Gearing, Natasha Jansz, Joy Liu, Aliaksei Z. Holik, Peter Hickey, Sarah Kinkel, Darcy Moore, Kelsey Breslin, Kelan Chen, Ruijie Liu, Chris Phillips, Miha Pakusch, Christine Biben, Julie Sheridan, Benjamin T. Kile, Catherine Carmichael, Matthew E. Ritchie, Douglas J. Hilton, Marnie E. Blewitt
Software Mentions: 8
Published: over 8 years ago
10.1186/s13062-016-0110-0
Altools: a user friendly NGS data analyserCited by: 5
Author(s): Salvatore Camiolo, Gaurav Sablok, Andrea Porceddu
Software Mentions: 7
Published: almost 9 years ago
10.7717/peerj.1796
Taxonomic revision of the Malagasy members of the<i>Nesomyrmex angulatus</i>species group using the automated morphological species delineation protocol NC-PART-clusteringCited by: 14
Author(s): Sándor Csősz, Brian L. Fisher
Software Mentions: 6
Published: over 8 years ago
10.1186/s12859-018-2299-7
CamurWeb: a classification software and a large knowledge base for gene expression data of cancerCited by: 9
Author(s): Emanuel Weitschek, Silvia Di Lauro, Eleonora Cappelli, Paola Bertolazzi, G. Felici
Software Mentions: 5
Published: about 6 years ago
10.1371/journal.pone.0010485
An Analysis of Genetic Changes during the Divergence of Drosophila SpeciesCited by: 13
Author(s): Rui Sousa‐Neves, Alexandre Rosas
Software Mentions: 4
Published: over 14 years ago
10.1038/srep38046
THD-Module Extractor: An Application for CEN Module Extraction and Interesting Gene Identification for Alzheimer’s DiseaseCited by: 10
Author(s): Tulika Kakati, Hirak J. Kashyap, Dhruba K. Bhattacharyya
Software Mentions: 4
Published: almost 8 years ago
10.1093/gigascience/giaa027
Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-CCited by: 43
Author(s): Matthew A. Field, Benjamin D. Rosen, Olga Dudchenko, Eva Chan, André E. Minoche, Richard J. Edwards, Kirston Barton, Ruth J. Lyons, Daniel Enosi Tuipulotu, Vanessa M. Hayes, Arina D. Omer, Zane Colaric, Jens Keilwagen, Ksenia Skvortsova, Ozren Bogdanović, Martin A. Smith, E Aiden, Timothy P. L. Smith, Robert A. Zammit, J. William O. Ballard
Software Mentions: 4
Published: over 4 years ago
10.1186/s13148-015-0135-8
Whole-genome bisulfite sequencing of cell-free DNA identifies signature associated with metastatic breast cancerCited by: 68
Author(s): Christophe Legendre, Gerald C. Gooden, Kyle N. Johnson, Rae Anne Martinez, Winnie S. Liang, Bodour Salhia
Software Mentions: 3
Published: about 9 years ago
10.1186/1471-2105-10-S12-S17
Protopia: a protein-protein interaction toolCited by: 11
Author(s): Alejandro Real-Chicharro, I. Ruiz-Mostazo, Ismael Navas‐Delgado, Amine Kerzazi, Othmane Chniber, Francisca Sánchez‐Jiménez, Miguel Ángel Medina, José F. Aldana‐Montes
Software Mentions: 3
Published: about 15 years ago
10.1038/srep35507
Historical dimensions of population structure in a continuously distributed marine species: The case of the endemic Chilean dolphinCited by: 8
Author(s): María José Pérez‐Álvarez, Carlos Olavarría, Rodrigo Moraga, C. Scott Baker, Rebecca M. Hamner, Élie Poulin
Software Mentions: 3
Published: about 8 years ago
10.1186/s13040-015-0067-z
BioDB extractor: customized data extraction system for commonly used bioinformatics databasesCited by: 2
Author(s): Rajiv Karbhal, Sangeeta Sawant, Urmila Kulkarni‐Kale
Software Mentions: 3
Published: over 9 years ago
10.1107/S0907444911054515
<i>PDB_REDO</i>: constructive validation, more than just looking for errorsCited by: 188
Author(s): Robbie P. Joosten, Krista Joosten, Garib N. Murshudov, Anastassis Perrakis
Software Mentions: 2
Published: over 12 years ago
10.1007/s12565-019-00506-1
Estimation of three-dimensional long axes of the maxillary and mandibular first molars with regression analysisCited by: 5
Author(s): Kazuto Terada, Takashi Kameda, Ikuo Kageyama, Makoto Sakamoto
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.pone.0237655
Development and evaluation of loop-mediated isothermal amplification for detection of Yersinia pestis in plague biological samplesCited by: 4
Author(s): Lovasoa Nomena Randriantseheno, Anjanirina Rahantamalala, Ando Lalaniaina Randrianierenana, Minoarisoa Rajerison, Voahangy Andrianaivoarimanana
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0224070
Proteomic characterisation of the Chlamydia abortus outer membrane complex (COMC) using combined rapid monolithic column liquid chromatography and fast MS/MS scanningCited by: 4
Author(s): David Longbottom, Morag Livingstone, Kevin Aitchison, Lisa Imrie, Erin Manson, Nick Wheelhouse, Neil F. Inglis
Software Mentions: 2
Published: about 5 years ago
10.12688/f1000research.3-18.v2
Mutation extraction tools can be combined for robust recognition of genetic variants in the literatureCited by: 26
Author(s): Antonio Jimeno-Yepes, Karin Verspoor
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0161963
Genetics, Gene Flow, and Glaciation: The Case of the South American Limpet Nacella mytilinaCited by: 13
Author(s): Claudio A. González‐Wevar, Sebastián Rosenfeld, Nicolás I. Segovia, Mathias Hüne, Karin Gérard, Jaime Ojeda, Andrés Mansilla, Paul Brickle, A Mendoza Diaz, Élie Poulin
Software Mentions: 2
Published: about 8 years ago
10.1186/1476-4598-6-50
In silico gene expression analysis – an overviewCited by: 47
Author(s): David Murray, Peter Doran, Padraic MacMathúna, Alan C. Moss
Software Mentions: 2
Published: over 17 years ago
10.1038/sdata.2018.1
A dataset of 200 structured product labels annotated for adverse drug reactionsCited by: 38
Author(s): Dina Demner‐Fushman, Sonya E. Shooshan, Laritza Rodriguez, Alan R. Aronson, F.M. Lang, Willie J. Rogers, Kirk Roberts, Joseph M. Tonning
Software Mentions: 2
Published: almost 7 years ago
10.1371/journal.pone.0000741
Genome Dynamics of Short Oligonucleotides: The Example of Bacterial DNA Uptake Enhancing SequencesCited by: 15
Author(s): Mohammed Bakkali
Software Mentions: 2
Published: over 17 years ago
10.1186/1751-0473-8-4
BlaSTorage: a fast package to parse, manage and store BLAST resultsCited by: 1
Author(s): Massimiliano Orsini, Simone Carcangiu
Software Mentions: 2
Published: almost 12 years ago
10.1186/1471-2105-7-390
PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence dataCited by: 29
Author(s): Kuo Ping Chiu, Chee-Hong Wong, Qiongyu Chen, Pramila Ariyaratne, Hong Ooi, Chia‐Lin Wei, Wing-Kin Sung, Yijun Ruan
Software Mentions: 2
Published: about 18 years ago
10.3389/frobt.2020.594412
End-to-End Automated Latent Fingerprint Identification With Improved DCNN-FFT EnhancementCited by: 1
Author(s): Uttam U. Deshpande, V. S. Malemath, Sandeep Patil, Sushma V. Chaugule
Software Mentions: 1
Published: almost 4 years ago
10.1007/s11357-018-0029-8
The association between relevant comorbidities and dementia in patients with atrial fibrillationCited by: 15
Author(s): Per Wändell, Axel C. Carlsson, Jan Sundquist, Kristina Sundquist
Software Mentions: 1
Published: over 6 years ago
10.1107/S0021889809008784
PDB_REDO: automated re-refinement of X-ray structure models in the PDBCited by: 197
Author(s): Robbie P. Joosten, Jean Salzemann, Vanessa Bloch, Heinz Stockinger, Asta Berglund, Clément E. Blanchet, Erik Bongcam‐Rudloff, Christophe Combet, Anna Luisa Costa, Gilbert Deléage, M. Diarena, R. Fabbretti, G. Fettahi, Volker Flegel, Andreas Gisel, Vinod Kasam, Tuomas Kervinen, Eija Korpelainen, Kimmo Mattila, Marco Pagni, Matthieu Reichstadt, Vincent Breton, Ian J. Tickle, Gert Vriend
Software Mentions: 1
Published: over 15 years ago
10.1371/journal.ppat.1006051
Integrated Activity and Genetic Profiling of Secreted Peptidases in Cryptococcus neoformans Reveals an Aspartyl Peptidase Required for Low pH Survival and VirulenceCited by: 26
Author(s): Starlynn Clarke, Phillip A. Dumesic, Christina M. Homer, Anthony J. O’Donoghue, Florencia La Greca, Lenka Pallová, Pavel Majer, Hiten D. Madhani, Charles S. Craik
Software Mentions: 1
Published: almost 8 years ago
10.1038/srep44559
Lineage divergence, local adaptation across a biogeographic break, and artificial transport, shape the genetic structure in the ascidian Pyura chilensisCited by: 16
Author(s): Nicolás I. Segovia, Cristian Gallardo‐Escárate, Élie Poulin, Pilar A. Haye
Software Mentions: 1
Published: over 7 years ago
10.3390/jimaging7040061
Time- and Resource-Efficient Time-to-Collision Forecasting for Indoor Pedestrian Obstacles AvoidanceCited by: 5
Author(s): David L. Urban, Alice Caplier
Software Mentions: 1
Published: over 3 years ago
10.1107/S0907444908037591
Re-refinement from deposited X-ray data can deliver improved models for most PDB entriesCited by: 56
Author(s): Robbie P. Joosten, Thomas Womack, Gert Vriend, G. Bricogne
Software Mentions: 1
Published: almost 16 years ago
10.1186/s12859-016-1396-8
Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sourcesCited by: 13
Author(s): Jin Mao, Lisa R. Moore, Carrine E. Blank, Elvis Hsin Hui Wu, Marcia Ackerman, Sonali Sachin Ranade, Hong Cui
Software Mentions: 1
Published: almost 8 years ago
10.1186/1471-2407-10-16
Stable alterations of CD44 isoform expression in prostate cancer cells decrease invasion and growth and alter ligand binding and chemosensitivityCited by: 22
Author(s): Kui Yang, Yaqiong Tang, Gabriel Habermehl, Kenneth A. Iczkowski
Software Mentions: 1
Published: almost 15 years ago
10.1186/1472-6947-9-S1-S3
An intelligent listening framework for capturing encounter notes from a doctor-patient dialogCited by: 17
Author(s): Jeffrey G. Klann, Peter Szolovits
Software Mentions: 1
Published: about 15 years ago
10.1186/1756-0500-7-379
BrassicaTED - a public database for utilization of miniature transposable elements in Brassica speciesCited by: 17
Author(s): Murukarthick Jayakodi, Sampath Perumal, Sang Choon Lee, Beom-Soon Choi, N. Senthil, Liu S, Tae-Jin Yang
Software Mentions: 1
Published: over 10 years ago
10.3390/life5031539
The Effects of Temperature and Growth Phase on the Lipidomes of Sulfolobus islandicus and Sulfolobus tokodaiiCited by: 30
Author(s): Sara Munk Jensen, Vinnie Lund Neesgaard, Sandra Landbo Nedergaard Skjoldbjerg, Martin Brandl, Christer S. Ejsing, Alexander H. Treusch
Software Mentions: 1
Published: about 9 years ago
10.3390/microorganisms7040098
The Cano-eMLST Program: An Approach for the Calculation of Canonical Extended Multi-Locus Sequence Typing, Making Comparison of Genetic Differences Among Bunches of Bacterial StrainsCited by: 1
Author(s): Yen‐Yi Liu, Ji-Wei Lin, Chih-Chieh Chen
Software Mentions: 1
Published: over 5 years ago
10.3390/molecules16010493
Tomato Polyphenol Oxidase B Is Spatially and Temporally Regulated during Development and in Response to EthyleneCited by: 26
Author(s): Sally Newman, Piyada Alisha Tantasawat, John C. Steffens
Software Mentions: 1
Published: almost 14 years ago
10.1016/j.vetpar.2016.03.008
A preliminary proteomic characterisation of extracellular vesicles released by the ovine parasitic nematode, Teladorsagia circumcinctaCited by: 42
Author(s): Thomas Tzelos, J. B. Matthews, Amy H. Buck, Fabio Simbari, David Frew, Neil F. Inglis, Kevin McLean, Alasdair J. Nisbet, Bruce Whitelaw, David P. Knox, Tom N. McNeilly
Software Mentions: 1
Published: over 8 years ago
10.14814/phy2.12180
Database of osmoregulated proteins in mammalian cellsCited by: 12
Author(s): Cameron R. Grady, Mark A. Knepper, Maurice B. Burg, Joan D. Ferraris
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pcbi.1002805
Chapter 3: Small Molecules and DiseaseCited by: 27
Author(s): David S. Wishart
Software Mentions: 1
Published: almost 12 years ago
10.1371/journal.pcbi.1005376
Elucidation of molecular kinetic schemes from macroscopic traces using system identificationCited by: 1
Author(s): Miguel Fribourg, Diomedes E. Logothetis, Javier González-Maeso, Stuart C. Sealfon, Belén Galocha Iragüen, Fernando Las-Heras, Vladimír Březina
Software Mentions: 1
Published: almost 8 years ago
10.1371/journal.pone.0037128
Analysis of Complete Nucleotide Sequences of 12 Gossypium Chloroplast Genomes: Origin and Evolution of AllotetraploidsCited by: 63
Author(s): Qi Xu, Guanjun Xiong, Pengbo Li, Fei He, Yi Huang, Kunbo Wang, Zhaohu Li, Jinping Hua
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pone.0138591
Proteomics of Aggregatibacter actinomycetemcomitans Outer Membrane VesiclesCited by: 48
Author(s): Thomas Kieselbach, Vincent Zijnge, Elisabeth Granström, Jan Oscarsson
Software Mentions: 1
Published: about 9 years ago
10.1371/journal.pone.0025781
Genomotyping of Coxiella burnetii Using Microarrays Reveals a Conserved Genomotype for Hard Tick IsolatesCited by: 17
Author(s): Quentin Leroy, Fabrice Armougom, Pascal Barbry, Didier Raoult
Software Mentions: 1
Published: about 13 years ago
10.1371/journal.pone.0077612
Glycolytic Metabolites Are Critical Modulators of Oocyte Maturation and ViabilityCited by: 7
Author(s): Lloyd C. Berger, Andrew Wilde
Software Mentions: 1
Published: about 11 years ago
10.1038/cddis.2013.221
Signal-dependent fra-2 regulation in skeletal muscle reserve and satellite cellsCited by: 19
Author(s): Nezeka S. Alli, Eric C. Yang, Tetsuaki Miyake, Arif Aziz, Henry Collins‐Hooper, Ketan Patel, John C. McDermott
Software Mentions: 1
Published: over 11 years ago
10.1016/j.dib.2016.12.015
Dataset of the proteome of purified outer membrane vesicles from the human pathogen Aggregatibacter actinomycetemcomintansCited by: 6
Author(s): Thomas Kieselbach, Jan Oscarsson
Software Mentions: 1
Published: almost 8 years ago
10.1093/database/baw031
RSIADB, a collective resource for genome and transcriptome analyses in<i>Rhizoctonia solani</i>AG1 IACited by: 18
Author(s): Lei Chen, Peng Ai, Jinfeng Zhang, Qi Deng, Yunlong Wang, Shuangcheng Li, Jun Zhu, Ping Li, Aiping Zheng
Software Mentions: 1
Published: almost 9 years ago
10.1186/1758-5996-6-2
Effects of prescribed antithrombotics and other cardiovascular pharmacotherapies on all-cause mortality in patients with diabetes and atrial fibrillation – a cohort study from Sweden using propensity score analysesCited by: 7
Author(s): Per Wändell, Axel C. Carlsson, Jan Sundquist, Sven‐Erik Johansson, Matteo Bottai, Kristina Sundquist
Software Mentions: 1
Published: almost 11 years ago
10.1155/2012/278652
The Cytotoxicity Mechanism of 6-Shogaol-Treated HeLa Human Cervical Cancer Cells Revealed by Label-Free Shotgun Proteomics and Bioinformatics AnalysisCited by: 21
Author(s): Qun Li, Yongbo Peng, Lian‐Wen Qi, Xiaolan Cheng, Xiaojun Xu, Lele Liu, E‐Hu Liu, Ping Li
Software Mentions: 1
Published: almost 13 years ago